[gmx-users] Fwd: how to add close proteins

Mark Abraham Mark.Abraham at anu.edu.au
Thu Feb 23 08:10:02 CET 2012

On 23/02/2012 5:46 PM, rama david wrote:
> Hi GROMACS users,
> I wish to study proteins behaviour,With the help of command
>  genbox -ci protein.gro -nmol <no of protein >.. -box <box size>
> -o <out put file> -p <topology file>   I am putting the four peptide
> at random positions, but I need to put theem close enough so they
>  are forming at least one hydrogen bond or at least enough close to
> start interact  immediately with one another ..
> I don´t wish to reduced by box size ...

Use editconf to rotate and translate your copies in their own coordinate 
files, and then concatenate them by hand - make sure you know how the 
file format works. Or do the foregoing in some molecule editor. Then 
solvate that.


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